Transom Bolt holes
 

I just finished putting in the new core for my transom. WHat is the best way to fill in the bolt holes that I made to clamp the core to the transom? Should I over drill and fill with thickened resin from the inside? I already patched the holes on the outside of the transom. or should I go the dowel route?

You might consider the epoxy stick stuff and jam it in with a dowel - just an idea

Thickened epoxy in a syringe or caulk tube should be fine. I use the WestSystems SIX10. Pricey at about $20 for half caulk tube but very effective. No fuss, no muss. use a conical or round grinding bit to give a tapered surface on the glass skin for best adhesion results.